zbfjk/atb2lammps

Convert files from the ATB repository to LAMMPS format

ATB to LAMMPS file converter

Use Python and Moltemplate to convert files from the ATB repository to LAMMPS format. Several examples are given here, including luteolin (video on the right), methane, or ethanol.

Use

Simply run atb2lammps.sh using bash:

bash atb2lammps.sh KIR7_allatom_optimized_geometry.lt

where KIR7_allatom_optimized_geometry.lt is the geometry file downloaded from the ATB. Then run LAMMPS:

lmp -in input.lammps

The dump file can be visualised using vmd:

vmd dump.lammpstrj

Alternative use:

Extract system.lt file

python3 extract_system_lt.py KIR7_allatom_optimized_geometry.lt

Execute moltemplate

moltemplate.sh system.lt

Create clean system

python3 clean_system.py

Delete extra files

rm -r output_ttree
rm system.*

run LAMMPS

lmp -in input.lammps